Variant report

Variant	rs3824878
Chromosome Location	chr11:94134472-94134473
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10741488	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10831222	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10831227	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11020774	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11523894	0.85[EUR][1000 genomes]
rs1257783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2155209	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3758787	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4459257	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs485146	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs491404	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs492073	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs514060	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs516037	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs534402	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs538800	0.87[EUR][1000 genomes]
rs541090	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs546439	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554715	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs556477	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs572372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs581449	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs583534	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs584531	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs592943	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs601391	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs604845	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs610611	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs618690	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs646130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs657830	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs661957	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523083	chr11:93962121-94150790	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832233	chr11:93981434-94158471	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3824878	RP11-685N10.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:94132600-94135200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
2	chr11:94132800-94134800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
3	chr11:94133000-94135000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
4	chr11:94133400-94135000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
5	chr11:94133800-94134800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr11:94133800-94134800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
7	chr11:94133800-94134800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:94133800-94134800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr11:94133800-94134800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr11:94133800-94134800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
11	chr11:94133800-94135000	Bivalent/Poised TSS	Fetal Brain Female	brain
12	chr11:94133800-94135000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
13	chr11:94133800-94135200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:94133800-94135200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:94133800-94135200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
16	chr11:94133800-94135400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr11:94133800-94135600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr11:94134000-94134600	Bivalent Enhancer	Esophagus	oesophagus
19	chr11:94134000-94134600	Bivalent Enhancer	Placenta	Placenta
20	chr11:94134000-94134600	Enhancers	Pancreas	Pancrea
21	chr11:94134000-94134600	Active TSS	Right Atrium	heart
22	chr11:94134000-94134800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr11:94134000-94134800	Bivalent/Poised TSS	NHDF-Ad	bronchial
24	chr11:94134000-94135000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr11:94134000-94135000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:94134000-94135000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:94134000-94135000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:94134000-94135000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:94134000-94135000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
30	chr11:94134000-94135000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:94134000-94135000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:94134000-94135000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:94134000-94135000	Bivalent/Poised TSS	Colonic Mucosa	Colon
34	chr11:94134000-94135000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
35	chr11:94134000-94135000	Bivalent/Poised TSS	HSMM	muscle
36	chr11:94134000-94135000	Bivalent/Poised TSS	HSMMtube	muscle
37	chr11:94134000-94135000	Bivalent/Poised TSS	NH-A	brain
38	chr11:94134000-94135000	Bivalent/Poised TSS	NHLF	lung
39	chr11:94134000-94135000	Bivalent/Poised TSS	Osteobl	bone
40	chr11:94134000-94135200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr11:94134000-94135200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:94134000-94135200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
43	chr11:94134000-94135200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:94134000-94135200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr11:94134000-94135200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:94134000-94135200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:94134000-94135200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:94134000-94135200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
49	chr11:94134200-94134600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
50	chr11:94134200-94134600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--

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